Tag qmmm [115 articles] Export

Recent papers classified by the tag qmmm.

	Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis [My Copy] Biochemistry, Vol. 48, No. 38. (29 September 2009), pp. 9061-9075. by Petra Imhof, Stefan Fischer, Jeremy C. Smith posted to qmmm enzyme by jmparks on 2009-10-06 18:58:02 as
	QM/MM Methods for Biological Systems [My Copy] Atomistic Approaches in Modern Biology (2007), pp. 173-290. by Hans Senn, Walter Thiel posted to review qmmm by moldyn_ich on 2009-09-11 21:13:51 as
	Modeling Reactive Scattering of F(2P) at a Liquid Squalane Interface: A Hybrid QM/MM Molecular Dynamics Study† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 26. (2 July 2009), pp. 7218-7226. by Brian K. Radak, Scott Yockel, Dongwook Kim, George C. Schatz posted to qmmm qm-mm by carlosjavierna on 2009-09-05 03:58:24 as
	The Protonation State of the Glu-71/Asp-80 Residues in the KcsA Potassium Channel: A First-Principles QM/MM Molecular Dynamics Study [My Copy] Vol. 93, No. 7. (1 October 2007), pp. 2315-2324. by Denis Bucher, Leonardo Guidoni, Ursula Rothlisberger posted to qmmm potassium dft by moldyn_ich on 2009-09-04 14:00:23 as
	Prediction and Rationalization of Protein pKa Values Using QM and QM/MM Methods [My Copy] The Journal of Physical Chemistry A, Vol. 109, No. 30. (1 August 2005), pp. 6634-6643. by Jan H. Jensen, Hui Li, Andrew D. Robertson, Pablo A. Molina posted to qmmm pka electrostatics by flbarroso on 2009-08-14 20:15:47 as
	Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. [My Copy] Annual review of physical chemistry, Vol. 59, No. 1. (2008), pp. 573-601. by H. Hu, W. Yang posted to enzyme free_energy qmmm by flbarroso on 2009-07-25 22:27:34 as along with 1 person skoddet
	Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity. [My Copy] Current topics in medicinal chemistry, Vol. 3, No. 11. (2003), pp. 1241-1256. by L. Ridder, A. J. Mulholland posted to enzyme qmmm simulation by flbarroso on 2009-07-25 22:26:33 as
	Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. [My Copy] The journal of physical chemistry. B, Vol. 110, No. 6. (16 February 2006), pp. 2934-2941. by E. Rosta, M. Klähn, A. Warshel posted to enzyme qmmm simulation by flbarroso on 2009-07-25 22:26:07 as
	Fixation of the Two Tabun Isomers in Acetylcholinesterase: A QM/MM Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 29. (23 July 2009), pp. 10001-10007. by Ophélie Kwasnieski, Laurent Verdier, Max Malacria, Etienne Derat posted to qm-mm qmmm by carlosjavierna on 2009-07-20 05:18:51 as
	Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies of a Prototypical Zinc Peptidase (Carboxypeptidase A) Suggest a General Acid−General Base Mechanism [My Copy] Journal of the American Chemical Society, Vol. 131, No. 28. (22 July 2009), pp. 9780-9788. by Dingguo Xu, Hua Guo posted to qm-mm qmmm by carlosjavierna on 2009-07-20 03:49:32 as
	pKa Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 37. (1 September 2005), pp. 17715-17733. by Demian Riccardi, Patricia Schaefer, Qiang Cui posted to pka qmmm by flbarroso on 2009-07-19 19:27:06 as along with 1 person qshao
	Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine ldquodipeptidesrdquo (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 50, No. 3. (15 February 2003), pp. 451-463. by Hao Hu, Marcus Elstner, Jan Hermans posted to force-fields peptide qmmm by flbarroso on 2009-07-19 02:20:03 as along with 3 people Diego_Prada paddydu allmensch
	Integrated Modeling Program, Applied Chemical Theory (IMPACT). [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1752-1780. by Jay L. Banks, Hege S. Beard, Yixiang Cao, et al.Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy posted to born mc md qmmm simulation by flbarroso on 2009-07-19 02:04:38 as along with 2 people oteri onufriev
	Solvent Effects on Global Reactivity Properties for Neutral and Charged Systems Using the Sequential Monte Carlo Quantum Mechanics Model [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4314-4322. by Paula Jaramillo, Patricia Pérez, Patricio Fuentealba, Sylvio Canuto, Kaline Coutinho posted to qmmm solvation by flbarroso on 2009-07-16 19:29:23 as along with 1 person goncalojustino
	Catalytic Mechanism of Diaminopimelate Epimerase: A QM/MM Investigation [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 7. (14 July 2009), pp. 1915-1930. by Marco Stenta, Matteo Calvaresi, Piero Altoè, et al.Domenico Spinelli, Marco Garavelli, Roberta Galeazzi, Andrea Bottoni posted to qm-mm qmmm by carlosjavierna on 2009-07-15 23:37:29 as
	Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Xiao He, Bing Wang, Kenneth M. Merz posted to merzkm proteins qm-mm qmmm by carlosjavierna on 2009-07-12 15:15:04 as along with 1 person and 1 group whitead Jiang Research Group
	A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems† [My Copy] The Journal of Physical Chemistry A, Vol. 0, No. 0. (0000) by Chris V. Sumowski, Christian Ochsenfeld posted to qm-mm qmmm by carlosjavierna on 2009-07-12 14:56:02 as
	QM/MM Study of the Second Proton Transfer in the Catalytic Cycle of the D251N Mutant of Cytochrome P450cam [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 28. (16 July 2009), pp. 9577-9588. by Muhannad Altarsha, Dongqi Wang, Tobias Benighaus, Devesh Kumar, Walter Thiel posted to qm-mm qmmm by carlosjavierna on 2009-07-11 14:56:06 as
	APT a next generation QM-based reactive force field model [My Copy] Molecular Physics, Vol. 105, No. 2. (2007), pp. 301-324. by A. K. Rappe, L. M. Bormann-Rochotte, D. C. Wiser, et al.J. R. Hart, M. A. Pietsch, C. J. Casewit, W. M. Skiff posted to esp forcefields modeling moleculardynamics parameterization qmmm transitionstate valence-bond by tovrstra on 2009-06-23 16:18:08 as along with 2 people daevans middledomain
	Multiscale methods for macromolecular simulations [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 5. (October 2008), pp. 630-640. by P. Sherwood, B. Brooks, M. Sansom posted to multiscale qmmm by xavierprat on 2009-05-29 17:18:37 as along with 6 people and 1 group jonathancooper flbarroso carlk aqeel choonpeng jmccammon McCammon
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to charmm qmmm by xavierprat on 2009-05-26 17:58:33 as along with 8 people and 1 group rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj saravan sobolevnrm dimka baker-group
	Does Water Relay Play an Important Role in Phosphoryl Transfer Reactions? Insights from Theoretical Study of a Model Reaction in Water and tert-Butanol [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 14. (9 April 2009), pp. 4930-4939. by Yang Yang, Qiang Cui posted to qmmm by xavierprat on 2009-04-29 16:47:38 as
	Microscopic pKa Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model† [My Copy] Biochemistry, Vol. 48, No. 11. (24 March 2009), pp. 2468-2485. by Nilanjan Ghosh, Xavier Prat-Resina, M. R. Gunner, Qiang Cui posted to qmmm by xavierprat on 2009-04-29 14:20:24 as along with 1 person and 1 group sobolevnrm baker-group
	A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein [My Copy] Journal of Computational Chemistry, Vol. 30, No. 8. (2009), pp. 1351-1359. by Yasuomi Kiyota, Jun-Ya Hasegawa, Kazuhiro Fujimoto, Ben Swerts, Hiroshi Nakatsuji posted to dynamics molecular qm qmmm by whitead to the group Jiang Research Group on 2009-04-24 16:02:38 as
	Evaluating Boundary Dependent Errors in QM/MM Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Iván Solt, Petr Kulhánek, István Simon, et al.Steven Winfield, Mike C. Payne, Gábor Csányi, Monika Fuxreiter posted to qmmm by charris5 on 2009-04-19 14:35:16 as
	Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package. [My Copy] J Phys Chem A (24 May 2007) by Gustavo D. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg posted to sccdftb qmmm amber by charris5 on 2009-04-17 14:55:50 as along with 3 people and 1 group krapnik vahmurk xdeupi LabCompMed
	A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters [My Copy] The Journal of Chemical Physics, Vol. 110, No. 6. (1999), pp. 2810-2821. by Glenn J. Martyna, Mark E. Tuckerman posted to qmmm pme by charris5 on 2009-04-17 00:35:08 as along with 1 person softsimu
	A dual length scale method for plane-wave-based, simulation studies of chemical systems modeled using mixed ab initio/empirical force field descriptions [My Copy] The Journal of Chemical Physics, Vol. 115, No. 8. (2001), pp. 3531-3539. by Dawn A. Yarne, Mark E. Tuckerman, Glenn J. Martyna posted to qmmm pme by charris5 on 2009-04-17 00:30:27 as
	Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Marius Retegan, Anne Milet, Hélène Jamet posted to bindingenergy kinaseinhibition md mmpbsa moleculardynamics qmmm by sschurer on 2009-04-13 21:31:21 as
	Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method [My Copy] The Journal of Chemical Physics, Vol. 129, No. 6. (2008), 064108. by Omololu A. Ojo, Yang Song, Feng Wang posted to adaptive afm dynamics field force md molecular qmmm by whitead to the group Jiang Research Group on 2009-04-09 19:50:31 as
	Improving the Point-Charge Description of Hydrogen Bonds by Adaptive Force Matching [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 5. (5 February 2009), pp. 1237-1240. by Omololu Akin-Ojo, Feng Wang posted to adaptive dynamics field force hydrogen-bonding md molecular qm qmmm by whitead to the group Jiang Research Group on 2009-04-09 19:35:31 as along with 1 person willard
	Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 12. (1 April 2009), pp. 4535-4540. by Yasushige Yonezawa, Kazuto Nakata, Kota Sakakura, Toshikazu Takada, Haruki Nakamura posted to pro proline qm-mm qmmm by carlosjavierna on 2009-03-30 14:17:19 as along with 1 person tprpip
	Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Pedro Fong, Jonathan P. Mcnamara, Ian H. Hillier, Richard A. Bryce posted to docking hiv qm-mm qmmm by carlosjavierna on 2009-03-30 04:43:16 as
	Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 5. (5 February 2009), pp. 1253-1272. by Shina C. L. Kamerlin, Maciej Haranczyk, Arieh Warshel posted to electrostatics pka qmmm by flbarroso on 2009-03-27 23:04:45 as along with 1 person xavierprat
	QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Paul M. Gleeson, Duangkamol Gleeson posted to qmmm by carlosjavierna on 2009-03-26 16:35:01 as along with 1 person middledomain
	Classical Fluctuating Charge Theories: The Maximum Entropy Valence Bond Formalism and Relationships to Previous Models† [My Copy] The Journal of Physical Chemistry A, Vol. 105, No. 12. (1 March 2001), pp. 2842-2850. by Jorge Morales, Todd J. Martinez posted to chargetransfer polarizable qmmm by tovrstra on 2009-03-25 13:48:21 as
	Ab initio QM/MM study of excited state electron transfer between pyrene and 4,4prime-bis(dimethylamino)-diphenylmethane with different solvent systems: Role of hydrogen bonding within solvent molecules [My Copy] International Journal of Quantum Chemistry, Vol. 102, No. 4. (2005), pp. 368-378. by Kakali Sen, Samita Basu, Dhananjay Bhattacharyya posted to qmmm by whitead to the group Jiang Research Group on 2009-03-20 18:04:07 as
	The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 7. (1 July 2008), pp. 1151-1161. by Martin J. Field posted to modeling qmmm by flbarroso on 2009-03-17 19:09:08 as
	A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 11, No. 6. (1990), pp. 700-733. by Martin J. Field, Paul A. Bash, Martin Karplus posted to qmmm by flbarroso on 2009-03-17 19:07:10 as
	Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 11. (19 March 2009), pp. 3280-3291. by Aaron M. Virshup, Chutintorn Punwong, Taras V. Pogorelov, Beth A. Lindquist, Chaehyuk Ko, Todd J. Martínez posted to qm-mm qmmm by carlosjavierna on 2009-03-15 16:42:15 as
	QM/MM Study of Thymidylate Synthase: Enzymatic Motions and the Temperature Dependence of the Rate Limiting Step† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 10. (12 March 2009), pp. 2176-2182. by Natalia Kanaan, Sergio Martí, Vicent Moliner, Amnon Kohen posted to arg cys molecular-modeling qm-mm qmmm by carlosjavierna on 2009-03-10 00:11:12 as
	QM/MM–MD simulation of hydrated vanadium(II) ion [My Copy] Chemical Physics Letters, Vol. 363, No. 3-4. (9 September 2002), pp. 367-371. by H. Loeffler posted to dynamics molecular qmmm by whitead to the group Jiang Research Group on 2009-03-05 18:20:09 as
	Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Pär Söderhjelm, Charlotte Husberg, Angela Strambi, Massimo Olivucci, Ulf Ryde posted to multpoles polarizability qmmm by middledomain on 2009-02-23 11:52:57 as
	Structural and energetic determinants of primary proton transfer in bacteriorhodopsin [My Copy] Photochem. Photobiol. Sci., Vol. 5, No. 6. (2006), pp. 547-552. by Ana-Nicoleta Bondar, Jeremy C. Smith, Stefan Fischer posted to back_isomerisation bacteriorhodopsin proton_pathways qmmm by vahmurk on 2009-02-08 23:06:11 as
	Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. [My Copy] Journal of molecular biology, Vol. 103, No. 2. (15 May 1976), pp. 227-249. by A. Warshel, M. Levitt posted to qmmm by xavierprat on 2009-02-02 15:47:13 as along with 2 people flbarroso sim82
	Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181 [My Copy] Journal of Molecular Biology, Vol. 383, No. 1. (31 October 2008), pp. 106-121. by K. Hall, T. Vreven, M. Frisch, M. Bearpark posted to 081218 qmmm rhodopsin spectrum by vahmurk on 2008-12-17 22:13:10 as
	<i>Ab initio</i>, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket [My Copy] Phase Transitions, Vol. 77, No. 1. (2004), pp. 31-45. by M. Sugihara, V. Buss, P. Entel, et al.J. Hafner, A. N. Bondar, M. Elstner, T. Frauenheim posted to 081218 md photoisomeration protein qm qmmm rhodopsin spectrum water by vahmurk on 2008-12-17 21:34:39 as
	Structures and spectral signatures of protonated water networks in bacteriorhodopsin. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 6980-6985. by G. Mathias, D. Marx posted to 081207 bacteriorhodopsin cpmd qmmm water by vahmurk on 2008-12-07 10:51:14 as along with 2 people and 1 group xdeupi saravan LabCompMed
	Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints [My Copy] Journal of Computational Chemistry, Vol. 24, No. 6. (2003), pp. 760-769. by Thom Vreven, Keiji Morokuma, Ödön Farkas, Bernhard H. Schlegel, Michael J. Frisch posted to 081118 bacteriorhodopsin method qmmm retinal spectrum uv by vahmurk on 2008-11-17 23:45:03 as
	Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method [My Copy] Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 109, No. 3. (18 April 2003), pp. 125-132. by T. Vreven, K. Morokuma posted to 081118 bacteriorhodopsin method opsin_shift qmmm retinal spectrum uv by vahmurk on 2008-11-17 23:40:25 as

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md	28
qm-mm	16
bacteriorhodopsin	12
rhodopsin	11
spectrum	11
protein	10
retinal	10
simulation	10
method	9
dynamics	8
gpcr	8
molecular	8
dft	7
enzyme	7
hartree-fock	7
zinc	7
mechanism	6
photoisomeration	6
structure	6
qm	5
adaptive	4
docking	4
field	4
force	4
light_absorption	4
periodic_boundary	4
polarizable	4
081218	3
electrostatics	3
myosin	3
peptide	3
pigments	3
pka	3
proton_pathways	3
warshel	3
081002	2
081006	2
081118	2
ab-initio	2
afm	2
f1-atpase	2
forcefield	2
gb	2
hiv-1_integrase	2
hydrogen-bonding	2
membrane	2
modeling	2
moleculardynamics	2
motor	2
multiscale	2
opsin_shift	2
organic_catalysis	2
pme	2
porphyrin	2
review	2
sccdftb	2
solvation	2
trp	2
uv	2
vdw	2
vision	2
water	2
081207	1
amber	1
arg	1
back_isomerisation	1
bindingenergy	1
charmm	1
chorismate	1
coulomb_screen	1
cpmd	1
cys	1
dna	1
drude	1
ecorv	1
esp	1
force-fields	1
forcefields	1
free_energy	1
fullatom	1
hiv	1
hyperpolarizability	1
internal_energy	1
kinaseinhibition	1
mc	1
mechanisms	1
mmpbsa	1
mutase	1
oniom	1
parameterization	1
polarization	1
potassium	1
prediction	1
pro	1
solvent_effects	1
spectroscopy	1
temperature-effect	1
theory	1
transitionstate	1
valence-bond	1

Tag qmmm [115 articles] Export

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